Error with latest Reactome and Netpath biopax files

[Ruth]

Hi,
I have been re-building my instance of cpath and the reactome and
Netpath biopax files keep coming up with the following error:

Reading in file: Mus musculus.owl
XML Type: BIO_PAX
Reading in meta-data from: db.info
Data source is: Reactome
Reading in file content...
Processing file...
Validating BioPAX File with Paxtools...
rethrew: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte UTF-8
sequence.

Is there any way of fixing the files?

It works fine for Cell map, Biocarta and NCI biopax files.

Thanks,
Ruth

[Gary Bader]

Hi Ruth - what do the top of the files look like in a text editor? Is
there an issue with them?

Gary

--
http://baderlab.org
Terrence Donnelly Centre for Cellular and Biomolecular Research
University of Toronto

[Ruth Isserlin]

Hi Gary,

The tops of the files don't look different to me. Reactome has a few more
things defined, not sure if that breaks them.

For Cellmap which works it looks like -
<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:bp="http:
//www.biopax.org/release/biopax-level2.owl#"
xmlns:owl="http://www.w3.org/2002/0
7/owl#" xmlns="http://cbio.mskcc.org/cpath#"
xml:base="http://cbio.mskcc.org/cpa
th">
<owl:Ontology rdf:about="">
<owl:imports
rdf:resource="http://www.biopax.org/release/biopax-level2.owl"
/>
</owl:Ontology>

And for Reactome it looks like -
<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:bp="http:
//www.biopax.org/release/biopax-level2.owl#"
xmlns:rdfs="http://www.w3.org/2000/
01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xsd="http://www
.w3.org/2001/XMLSchema#" xmlns="http://www.reactome.org/biopax#"
xml:base="http:
//www.reactome.org/biopax">
<owl:Ontology rdf:about="">
<owl:imports
rdf:resource="http://www.biopax.org/release/biopax-level2.owl"
/>
</owl:Ontology>

Thanks,
Ruth

[Gary Bader]

I think you have to use a hex editor to see the if the actual bytes are
different.

Gary

[Ethan Cerami]

I think that Ben uses a character conversion utility to fix this issue, but he is on holiday today (it's the fourth of july vacation here today).

[rex....@syngenta.com]

I am having similar problems trying to read reactome files in BP level 3 programmatically with paxtools.

I don’t understand – is this a bug in paxtools, or do the files need to be rebuilt with the right character set or something?

Does anyone know of level 3 files in the correct format?

Rex

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